A couple of things I can think of:
1. Did you silicon both the seal/metal and seal/glass areas?
2. Does the top of your frame have mounting holes for either a soft top, or bikini? When I recently removed my windshield frame, I realized the holes for my bikini channel were allowing water inside the frame, when I run the hardtop and have to remove the channel.
3. Are you sure it's not the cowl seal that's leaking? Mine had leaks at both the glass seal and cowl seal.
Here's a few shots of mine, before and after I painstakingly treated all the rust, and then metal glazed and sanded for paint.